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October 2005 GMOD Meeting

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Generic Model Organism Database Construction Set


Meeting 7

Thursday, October 27, 2005 Gerry Conference Room, Marks Building, CSHL


Agenda

9:10am Introductions
Scott Cain, GMOD coordinator
9:30 GMOD/chado 0.003 and roadmap, including:
  • improvements for next release
  • standardizing chado use across orgs
  • upgrade paths (script to modify data and schema?)
  • other topics that should be discussed during this meeting
10:30 Break
10:45 Top ten things a MOD provides
more on the road map; how Chado, GBrowse, Turnkey and Apollo fit in and where the holes are
12:00 Lunch
1:30 architecture working group: Review and revisit what we have done
2:00 Testing Recommendations
2:45 Break
3:00 Java O/R recommendation
3:30 Discussion: other topics, either architecture or other software issues
Friday, October 28, 2005
DIFFERENT ROOM: Plimpton Conference Room, Beckman Building, CSHL
9:10 Common URLs and common gene page
10:30 Break
12:00 Lunch
1:30 Revisiting the developer's guide; preparing a software package for release
2:00 Software demos, coffee

Meeting Report

Meeting report for October, 2005 GMOD meeting. This is an outline by Scott Cain.

Topics covered:

  • Current state of gmod/chado release, movement towards 0.1 release
  • Discussed 'MOD Top Ten list'
    • Mike Cherry proposed operating a MOD 'co-location' facility with all GMOD tools. The may be greatly facilitated by the software packaging work done by Allen Day and Brian O'Connor with biopackages.net.
    • Some discussion of using a content management tool like Drupal to handle some of the page display tasks for a MOD and use turnkey only as a tool to access and display chado related data.
  • Architecture
    • Testing recommendations
    • Volunteers to examine Java ORMs Hibernate and iBatis
    • How to get various chado instances to conform to a standard method of encoding data? Documentation: Joshua (TIGR) volunteered to document how TIGR is using chado to encode data and make it public as a first step in a collaborative effort among current users of chado (including TIGR, FlyBase, and GMOD developers).
  • www.gmod.org
    • In the evening of the first day, Allen Day, Brian O'Connor and Scott Cain created a prototype website with the purpose of improving the function of the site. It is based on an open source content management software package that will facilitate collaborative documentation projects, such as the chado usage project discussed earlier that day.
  • Common gene page. Since this group does not represent the target users, we did not feel that we would make much headway in establishing a standard. However, it was noted that the data collected by GO for several organisms contains much of the data that would be needed for a simple gene page. It was decided that Scott Cain would create a gene page using this data and present it at the biocurators meeting in December
  • Software developer's guide and software release recommendations
  • stuff to do
    • Scott: build sample gene page from GO gene data (or talk Chris into doing it) hopefully to present to biocurator list in December
    • Migrate website to facilitate documentation improvements
    • key to improving standards for chado usage
    • follow up on getting/comparing data dumps for different chado implementations
    • Talk to lincoln about identifying a journal for publication
  • demos